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<div class="title">moltk/Aligner.hpp</div>  </div>
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<a href="Aligner_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    Commercial users should ask about our dual licensing model.</span>
<a name="l00020"></a>00020 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00021"></a>00021 <span class="comment">*/</span>
<a name="l00022"></a>00022 
<a name="l00028"></a>00028 <span class="preprocessor">#ifndef MOLTK_ALIGN_ALIGNER_H</span>
<a name="l00029"></a>00029 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_ALIGN_ALIGNER_H</span>
<a name="l00030"></a>00030 <span class="preprocessor"></span>
<a name="l00031"></a>00031 <span class="preprocessor">#include &quot;<a class="code" href="DPTable_8hpp.html" title="Templated classes encapsulating dynamic programming sequence alignment algorithms.">moltk/DPTable.hpp</a>&quot;</span>
<a name="l00032"></a>00032 
<a name="l00033"></a><a class="code" href="namespacemoltk.html">00033</a> <span class="keyword">namespace </span>moltk {
<a name="l00034"></a>00034 
<a name="l00038"></a><a class="code" href="classmoltk_1_1Aligner.html">00038</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> 
<a name="l00039"></a>00039 {
<a name="l00040"></a>00040 <span class="keyword">public</span>:
<a name="l00041"></a>00041 
<a name="l00042"></a>00042     <span class="comment">// typedef moltk::units::Information Information;</span>
<a name="l00043"></a>00043 
<a name="l00044"></a>00044 <span class="keyword">public</span>:
<a name="l00046"></a>00046     <a class="code" href="classmoltk_1_1Aligner.html#a99008604e446e2adc4f0df7e4afd6c9e" title="Construct an Aligner with default parameters and no Alignments yet.">Aligner</a>();
<a name="l00047"></a>00047     <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> <a class="code" href="classmoltk_1_1Aligner.html#a12bd197b84d50d7c1e8f952c91eb7666">align</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp;, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp;);
<a name="l00049"></a><a class="code" href="classmoltk_1_1Aligner.html#a92f546677ff4bd7349fe45ee108a3149">00049</a>     <span class="keyword">const</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html">MatrixScorer</a>&amp; <a class="code" href="classmoltk_1_1Aligner.html#a92f546677ff4bd7349fe45ee108a3149" title="scorer computes alignment scores.">get_scorer</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">scorer</a>;}
<a name="l00051"></a><a class="code" href="classmoltk_1_1Aligner.html#ac60b7a16b4d99c7af16bfcfb9989dc00">00051</a>     <a class="code" href="classmoltk_1_1MatrixScorer__.html">MatrixScorer</a>&amp; <a class="code" href="classmoltk_1_1Aligner.html#ac60b7a16b4d99c7af16bfcfb9989dc00" title="MatrixScorer object this Aligner uses to score alignments.">get_scorer</a>() {<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">scorer</a>;}
<a name="l00052"></a><a class="code" href="classmoltk_1_1Aligner.html#afac71af10ee7a0436853ae03b38f02dc">00052</a>     <a class="code" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a>&amp; <a class="code" href="classmoltk_1_1Aligner.html#afac71af10ee7a0436853ae03b38f02dc">set_scorer</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html">MatrixScorer</a>&amp; <a class="code" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">scorer</a>) {this-&gt;scorer = <a class="code" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">scorer</a>; <span class="keywordflow">return</span> *<span class="keyword">this</span>;}
<a name="l00053"></a>00053 
<a name="l00057"></a>00057     <span class="keyword">static</span> <a class="code" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a>&amp; <a class="code" href="classmoltk_1_1Aligner.html#a2a94cf962985576ec14640ee519fa371" title="Global shared aligner object used by align() method.">get_shared_aligner</a>();
<a name="l00058"></a>00058 
<a name="l00060"></a><a class="code" href="classmoltk_1_1Aligner.html#a683da4069fec5bc5b2766792b8f37c04">00060</a>     dp::DPTable&lt;moltk::units::Information, dp::DP_MEMORY_LARGE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, 1&gt; <a class="code" href="classmoltk_1_1Aligner.html#a683da4069fec5bc5b2766792b8f37c04" title="The actual dynamic programming table.">test_table</a>;
<a name="l00061"></a>00061 
<a name="l00062"></a>00062 <span class="keyword">protected</span>:
<a name="l00063"></a><a class="code" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">00063</a>     <a class="code" href="classmoltk_1_1MatrixScorer__.html">MatrixScorer</a> <a class="code" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">scorer</a>;
<a name="l00064"></a>00064 };
<a name="l00065"></a>00065 
<a name="l00066"></a>00066 <span class="comment">/*</span>
<a name="l00067"></a>00067 <span class="comment"> * global align() methods helps get SEQUOIA-like conciseness in python.</span>
<a name="l00068"></a>00068 <span class="comment"> */</span>
<a name="l00069"></a>00069 <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a> <a class="code" href="namespacemoltk.html#a403bc85428d8dd3e1b17e60f2968dc1d">align</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; target_alignment, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; query_alignment);
<a name="l00070"></a>00070 
<a name="l00071"></a>00071 } <span class="comment">// namespace moltk</span>
<a name="l00072"></a>00072 
<a name="l00073"></a>00073 <span class="preprocessor">#endif // MOLTK_ALIGN_ALIGNER_H</span>
<a name="l00074"></a>00074 <span class="preprocessor"></span>
</pre></div></div>
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